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This is the working version of the Biological Collections Ontology, which was originally created at the Biocode Commons Hackathon at GSC14. Older versions can be viewed at http://code.google.com/p/biocode-commons/source/browse/#svn%2Ftrunk%2Fontologies%2Fbiocollections. Some of the classes in this ontology may be replaced by existing or newly requested terms from OBI or other ontologies.Biocode Commons Ontology Hackathon membersBarry SmithRamona Wallsevidence roleCan come from OBIpersistent evidence rolefalsetrueAn evidence role that persists through time.Could add relation that persistant evidence role is specifically dependent on a museum material samples.
Deprecated because we do not need this term. Can use OBI:evidence role. Not clear what it means for an evidence role to persist through time.collecting processRW: I think this term is now redundant with material sampling process.observing processThe information artifact may written or recorded or just be stored in someone's head (specifically depenedent upon that person).
Question: Is a trip camera capture of a jaguar an observation?A planned process in which a person or machine sees a material entity and that has as output an information content entity about that material entity.being there processA process of existing in a particular spatio-temporal region.We can probably deprecate this term.
printed reportThis class may be less important for modeling collection data, but could be important for efforts to get hand written (specifically dependent) reports into an electronic (generically dependent) report, and monitoring that process.printed observational reportNo more relation inverse depends on. Need to figure out correct relation.A printed report that inverse depends on a process of observing.selecting processA planned process by which a person or machine decides that a particular material entity as worthy of collection.submitting processA planned process whereby a person submits a material sample to an organization.Examples include a curator submitting a herbarium speciman to a museum, or a researcher submitting a water sample to a laboratory storage collection.physical extraction processConsidered aquisition in OBI, but that is about taking possession. Physical extraction may involve taking pocession, but it may also just involve extraction (e.g. of dna from cells). A planned process that involved removing a material sample from one site to another. Examples include removing a fish from the ocean with a net, removing dna from cells, picking leaves from a plant.material sampling processUse term from OBIdata sampling processOBI would classify this as an assay. Use OBI term.statistical sampling processWork with OBI on their treatment of statistical sampling.locality descriptionAn information artifact that is about a spatio-temporal region at which a process (such as collecting process, observing process, or material sampling process) occured.The 'is about' relation is the property used in the IAO between an information content entity and some other entity. This relation does not exist in BFO. This may be an special case of 'has generic dependence at some time'.
Someone asked "Why not just use site?" Darwin Core needs to describe both the site and time where some activity occurred as an information content entity (e.g., data from a lab notebook). Should look into whether site is better than spatio-temporal region.material sample roleA role that inheres in some material entity as a result of the output of some material sampling process.By virtue of the existance of the material sample, we know that the sampling process was successful.successful material sampling processtrueA sampling process that has as output some material sample.Do not need this class. By virtue of the existance of the material sample, we know that the sampling process was successful.unsuccessful material sampling processtrueDo not need this class. By virtue of the absence of the material sample, we know that the sampling process was unsuccessful.A material sampling process that has as output exactly zero material samples.museum collection entitytrueorganismal museum collection entitytrueA museum collections entity that derives from an organismal entity, has a persistent evidence role and 'depends on' a process of collecting.The label for this on the original diagram was 'collection object'. However, not all entities in collections will fit the defition of 'object', so 'collection entity is probably a better name.
The relation 'depends on' cannot really be used here. Old BFO has 'inverse depends on', but this is not in the current BFO. See dwc_bfo2_new.owl for the original logical definition.museum collectionAn object aggregate that has as part a material sample that is located in museum as a result of a process of curation.Intent is to document biodiversity. Use for research and education.organismal museum collectionA museum collection that has as part a organismal material sample.institutiontrueWill be replaced by OBI organization. Request institution as synonym.organismal entitytrueA material entity that derives from an organism or virus or viroid.This class is understood to mean: A material entity that is either an organism, a part of an organism, a collection of organisms, or a fossil.
The relation 'organismal entity derives from organism' was in the original diagram. Subclasses of organismal entity include organism, and It is not clear if it is valid to that an organism derives from an organism (is the derives from relation reflexive?).organism or virus or viroidThis terms will be replaced by a term imported from CARO.
The original diagram only had organsim, but DWC and GOs both need to include viruses and viroids.material sampleA material entity that has a material sample role.Example: A jar of water, the microbes that were filtered from that water, the DNA extracted from those microbes, a subsample of that DNA.
Still need to create the relations between material sample role and successful material sampling process.
This is already in OBI.data sampleAn information content entity (?) that is the result of some data sampling process.statistical samplereplace with term from OBIprotocol governed sampling activitytrueIf sampling is a OBI planned process, that captures that it is protocal governed.identification processA process by which a material sample is associated with a taxon.process that yields a material representation of a material entityIncludes as output rubbings, casts, photographic prints, audio or video tapes.
Needs a better name. Current name is the definition.material target of observationA material entity that has a target of observation role.This could either be defined as a material entity that specified input of some observing process OR as a material entity that has a target of observation role. Target of observation role would be defined similarly to material sample role.process that yields an information artifact that is a representation of a material entityIncludes audio recordings and photographs (which are information artifacts).
Needs a better name. Current name is the definition.material target of observation roleA role that inheres in some material entity as a result of the output of some observing process.